An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5

ABSTRACT

Short linear motifs, known as LC3-interacting regions (LIRs), interact with mactoautophagy/autophagy modifiers (Atg8/LC3/GABARAP proteins) via a conserved universal mechanism. Typically, this includes the occupancy of 2 hydrophobic pockets on the surface of Atg8-family proteins by 2 specific aromatic and hydrophobic residues within the LIR motifs. Here, we describe an alternative mechanism of Atg8-family protein interaction with the non-canonical UBA5 LIR, an E1-like enzyme of the ufmylation pathway that preferentially interacts with GABARAP but not LC3 proteins. By solving the structures of both GABARAP and GABARAPL2 in complex with the UBA5 LIR, we show that in addition to the binding to the 2 canonical hydrophobic pockets (HP1 and HP2), a conserved tryptophan residue N-terminal of the LIR core sequence binds into a novel hydrophobic pocket on the surface of GABARAP proteins, which we term HP0. This mode of action is unique for UBA5 and accompanied by large rearrangements of key residues including the side chains of the gate-keeping K46 and the adjacent K/R47 in GABARAP proteins. Swapping mutations in LC3B and GABARAPL2 revealed that K/R47 is the key residue in the specific binding of GABARAP proteins to UBA5, with synergetic contributions of the composition and dynamics of the loop L3. Finally, we elucidate the physiological relevance of the interaction and show that GABARAP proteins regulate the localization and function of UBA5 on the endoplasmic reticulum membrane in a lipidation-independent manner.

Abbreviations: ATG: AuTophaGy-related; EGFP: enhanced green fluorescent protein; GABARAP: GABA-type A receptor-associated protein; ITC: isothermal titration calorimetry; KO: knockout; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NMR: nuclear magnetic resonance; RMSD: root-mean-square deviation of atomic positions; TKO: triple knockout; UBA5: ubiquitin like modifier activating enzyme 5     

Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Basic pancreatic trypsin inhibitor

The assignment of the ¹H nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor with the use of two-dimensional ¹H nuclear magnetic resonance techniques at 500 MHz is described. The assignments are based entirely on the known amino acid sequence and the nuclear magnetic resonance data. Individual resonance assignments were obtained for all backbone and C^β protons, with the exception of those of Arg1, Pro2, Pro13 and the amide proton of Gly37. The side-chain resonance assignments are complete, with the exception of Pro2 and Pro13, the N^δ protons of Asn44 and the peripheral protons of the lysine residues and all but two of the arginine residues.     

Identification of clathrin heavy chain as a direct interaction partner for the gamma-aminobutyric acid type A receptor associated protein

Gamma-aminobutyric acid type A receptors (GABAA receptors) are the major sites of GABA-mediated fast synaptic inhibition in the central nervous system. Variation of the cell surface receptor count is postulated to be of importance in modulating inhibitory synaptic transmission. The GABAA receptor associated protein (GABARAP) is a ubiquitin-like modifier, implicated in GABAA receptor clustering, trafficking, and turnover. GABARAP pull-down experiments with brain lysate identified clathrin heavy chain to be GABARAP-associated. Phage display screening of a randomized peptide library for GABARAP ligands yielded a sequence motif which characterizes the peptide binding specificity of GABARAP. Sequence database searches with this motif revealed clathrin heavy chain as a protein containing the identified sequence motif within its residues 510-522, supporting the result of the pull-down experiments. Calreticulin, which was identified recently as a GABARAP ligand, contains a very similar sequence motif. We demonstrate that calreticulin indeed competes with clathrin heavy chain for GABARAP binding. Finally, employing nuclear magnetic resonance spectroscopy, we mapped the GABARAP residues responsible for binding to clathrin. The hereby mapped GABARAP regions overlap very well with the homologue residues in yeast Atg8 that were recently shown to be important for autophagy. Together with the knowledge that GABARAP and clathrin are known to be involved in GABAA receptor trafficking within the cell, this strongly suggests a clear physiological relevance of the direct interaction of GABARAP with clathrin heavy chain.     

Protein-lipid interactions glycophorin and dipalmitolyphosphatidylcholine.

The choline methyl groups of dipalmitoylphosphatidylcholine were enriched with ¹³C, and glycophorin extracted from human erythrocytes was included in bilayers of this phospholipid. At temperatures below the transition temperature, the ¹³C nuclear magnetic resonance spectra have two components, one sharp and one broad. The sharp signal is attributed to relatively “fluid” lipids in the immediate vicinity of the glycoprotein. In a defined ternary mixture consisting of ¹³C-labeled dipalmitoylphosphatidylcholine, dielaidoylphosphatidylcholine and glycophorin, the sharp ¹³C resonance signal disappears below the transition temperature of the mixture, indicating that the unsaturated lipid is preferentially associated with the glycoprotein under these conditions.     

Dielectric measurements on live biological materials under magnetic resonance conditions

In the course of work on the interactions of electric and magnetic fields with both living and dead biological materials, it was noticed that certain published dielectrophoretic yield curves for biological cells showed unexplained deviations in the region of 2 kHz. Dielectrophoretic measurements made at frequencies and magnetic fields which satisfied the nuclear magnetic resonance conditions showed sharply resonant features. Dielectric measurements showed small, but sharp, resonances most easily seen in the dielectric loss curves which had a bandwidth of the order of one Hertz and presented at the frequencies which satisfied the magnetic resonance conditions for the ambient magnetic field. Resonances were found corresponding to the frequencies for electron spin resonance and nuclear magnetic resonance for¹H,³¹P,²³Na,³⁷Cl and³⁹K. The onset of these resonances occurs at the value of the steady magnetic field strength so that one quantum of magnetic flux (2.07×10^?15wb) would link a single biological cell or pair of cells, approximately 1 G (100μT) in the case of a 5-μm yeast cell. The effects of these magnetic resonance conditions on the mean generation time ofE. coli and on the reaction of the enzyme lysozyme with the substrateM. lysodeikticus cells are also shown.     

Author index for volume 181, number 2

A phosphodiester, which comes into resonance at 0.4 ppm in the ³¹P nuclear magnetic resonance spectrum of intact muscles, has been isolated from the pectoralis muscle of chickens with hereditary muscular dystrophy by perchloric acid extraction, barium and alcoholic fractionation, and chromatographic isolation procedures. The compound,l-serine ethanolamine phosphodiester, whose presence is a characteristic of the diseased chicken muscle, has been characterized by ³¹P, ¹³C, and ¹H nuclear magnetic resonance as well as by chemical and chromatographic procedures.     

Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra: Glucagon bound to perdeuterated dodecylphosphocholine micelles

The assignment of the ¹H nuclear magnetic resonance spectrum of glucagon bound to perdeuterated dodecylphosphocholine micelles with the use of two-dimensional ¹H nuclear magnetic resonance techniques at 360 MHz is described. Sequential resonance assignments were obtained for all backbone and C^β protons except the N-terminal amino group and the amide proton of Ser2. The assignments of the non-labile amino acid side-chain protons are complete except for the γ-methylene protons of Gln20 and Gln24. These assignments provide a basis for the determination of the three-dimensional structure of lipid-bound glucagon.     

Determination of the mode of interaction of Mn2+ and Cu2+ with cis-inositol by 13C NMR spectroscopy

Natural abundance ¹³C nuclear magnetic resonance spectroscopy (¹³C NMR) was used to study the mode of binding of Mn²⁺ and Cu²⁺ to the cyclitol, cis-inositol. Resonance linewidths and the electron nuclear relaxation rates [(T₁^e)^?1 values] were used to establish that a unique binding site exists for these metal-ions on this cyclitol involving only the three axial hydroxyl groups. This work may aid in the development of new organometallic complexes used as paramagnetic relaxation agents in magnetic resonance imaging research.     

Solution structure of human GABA(A) receptor-associated protein GABARAP: implications for biolgoical funcrion and its regulation

Control of neurotransmitter receptor expression and delivery to the postsynaptic membrane is of critical importance for neural signal transduction at synapses. The gamma-aminobutyric acid, type A (GABA(A)) receptor-associated protein GABARAP was reported to have an important role for movement and sorting of GABA(A) receptor molecules to the postsynaptic membrane. GABARAP not only binds to GABA(A) receptor gamma2-subunit but also to tubulin, gephyrin, and ULK1. We present for the first time the high resolution structure of human GABARAP determined by nuclear magnetic resonance in aqueous solution. One part of the molecule, despite being well ordered and rigid on a MHz time scale, exists in at least two different conformations that interchange with each other on a time scale slower than 25 Hz. An important feature of the solution structure is the observation that amino- and carboxyl-terminal ends of the protein directly interact with each other, which is not seen in recently reported crystal structures. The possible biological relevance of these observations for the regulation of GABARAP interactions and functions is discussed.     

Quantitative determination of conformations of flexible molecules in solution using lanthanide ions as nuclear magnetic resonance probes: application to adenosine-5'-monophosphate

A procedure is described here whereby the conformation, of a flexible molecule in solution can be found. The method depends on the study of the nuclear magnetic resonance spectrum of the molecule in the presence of perturbations due to specifically bound lanthanide cations. The magnetic perturbations are of two kinds: shifts of nuclear magnetic resonance spectral lines in the presence of cations such as Eu³⁺ and changes in relaxation rates of the nuclear magnetic resonance excitations in the presence of cations such as Gd³⁺. Suitable expressions are given for the relation between the magnitude of the perturbations and the geometry of the lanthanide complex in the absence of through-bond perturbations and for an axially symmetric system. It is proved that the spectral changes described here are not due to through-bond (contact) effects. The circumstances, in which the anisotropy of the magnetic susceptibility tensor, as seen in the nuclear magnetic resonance spectra, is of axial symmetry, are defined. The experimental systems described are of this kind. A computer program has been devised that searches for the conformations of the molecule which fit the nuclear magnetic resonance data.We outline here the principles of the method and how we have used a combination of relaxation and shift probes to obtain the conformation of adenosine-5′-monophosphate at pH 2. It is shown that a small family of closely related conformations fit the nuclear magnetic resonance data. These conformations are very similar to that of the crystal structure of AMP.     

Dynamics of B-DNA in the solid state

Hydrated solid B-form DNA is shown to have large amplitude motions of the phosphodiester groups and immobile bases at temperatures above 5 °C. The ³¹P nuclear magnetic resonance chemical shift powder pattern of DNA in the solid state is significantly averaged by motions that are rapid compared to 10⁴ Hz. The DNA was labelled with deuterium at the C-8 purine position by exchange. The ²H nuclear magnetic resonance spectra have complete static quadrupole powder patterns indicative of no motions fast compared to 10⁶ Hz at 50 °C.     

Regeneration in Alfalfa Tissue Culture: Characterization of Intracellular pH During Somatic Embryo Production by Solid-State P-31 NMR

The composition of phosphorus-containing compounds of intact lyophilized alfalfa tissue has been determined, in part, by solid-state ³¹P nuclear magnetic resonance. The tissue (Medicago sativa L., cv Regen S; and some of its crosses) was grown in culture under both nonregenerating and regenerating conditions, the latter enhanced by the addition of specific amino acids. Analysis of the ³¹P nuclear magnetic resonance spectra shows that regeneration is favored when metabolism occurs without the production of a low average intracellular pH.     

C-terminal processing of GABARAP is not required for trafficking of the angiotensin II type 1A receptor

ObjectiveGABARAP, a small (117 aa) trafficking protein, binds to the C-terminal, cytoplasmic domain of rat angiotensin type-1A receptor (AT₁R), the predominant effector of the octapeptide angiotensin II (Ang II) (Cook et al., Circ. Res. 2008;102:1539–47). The objectives of this study were to map the interaction domains of GABARAP and AT₁R, to determine the effect of GABARAP association on AT₁R signaling activity, and to determine the importance of post-translational processing of GABARAP on accumulation of AT₁R on the plasma membrane and its signaling function.ResultsDeletion analysis identified two regions within GABARAP necessary for interaction with AT₁R in yeast two-hybrid assays: 1) a domain comprised of residues 32–51 that is nearly identical to that involved in binding and intracellular trafficking of the GABA_A receptor and 2) a domain encompassing the C-terminal 21 aa. The GABARAP interaction domain of AT₁R was delimited to the 15 aa immediately downstream of the last membrane spanning region. Overexpression of GABARAP in rat adrenal pheochromocytoma PC-12 cells increased the cell-surface expression of AT₁R and Ang II-dependent activation of the cAMP signaling pathway. Residues within AT₁R necessary for these responses were identified by mutational analysis. In PC-12 cells, GABARAP was constitutively and quantitatively cleaved at the C-terminus peptide bond and this cleavage was prevented by mutation of Gly¹¹⁶. Wild-type GABARAP and the G116A mutant were, however, equally effective in stimulating AT₁R surface expression and signaling activity.ConclusionsGABARAP and AT₁R interact through discrete domains and this association regulates the cell-surface accumulation and, consequently, ligand-induced function of the receptor. Unlike that observed with the GABA_A receptor, this regulation is not dependent on C-terminal processing and modification of GABARAP.     

Characterization of micellar-packaged gramicidin A channels.

The effects of heating, on an aqueous gramicidin A lysolecithin system, were examined by carbon-13 nuclear magnetic resonance (¹³C-NMR), circular dichroism (CD), and sodium-23 nuclear magnetic resonance (²³Na-NMR), and the results are collectively interpreted to indicate micellar-packaging of gramicidin channels and cation occupancy in the channel. ¹³C-NMR of the gramicidin-lysolecithin system demonstrates a decrease in mobility of the micellar lipid on heating which is indicative of incorporation of gramicidin into the hydrophobic core of the micelle. A unique and reproducible CD spectrum is obtained for the heat incorporated state. Sodium-23 spin-lattice relaxation times (T₁) demonstrated sodium interaction to be dependent on heat incorporation. The T₁ identified interaction is blocked by silver ion which is known to block sodium transport through the channel in lipid bilayer studies. The temperature dependence of the sodium-23 line width defines an exchange process with an activation energy of 6.8 kcal/mole which is essentially the same as the activation energy reported for transport through the channel in lecithin bilayer studies, and the sodium exchange process is blocked by thallium ion which is also known to block sodium transport through the channel.     

Differential mobility of the N-terminal headpiece in the lac-repressor protein.

It is shown by resolution enhancement and relaxation studies of the 360 MHz ¹H nuclear magnetic resonance spectra of the lac-repressor of Escherichia coli and the two fragments derived from it by limited tryptic digestion (the N-terminal headpiece and remaining T-core) that the majority of the relatively mobile residues in the intact lac-repressor are located in the headpiece. Although nuclear magnetic resonance data clearly indicate that the headpiece is a highly structured entity, even when isolated, it is a more mobile part of the repressor than the T-core.     

Quadrupole Relaxation of the 7Li+ Ion in Dilute Aqueous Solution Determined by Experimental and Theoretical Methods

A combination of molecular dynamics simulations (MD), ab initio selfconsistent field (SCF) calculations and nuclear magnetic resonance relaxation time experiments (NMR) is a powerful battery of techniques to investigate the molecular origins of the nuclear quadrupole relaxation mechanism for ⁷Li⁺ ions in dilute aqueous solution.     

Structural and mode of action studies on bio-active molecules

The technique of nuclear Overhauser effect difference spectroscopy allows the determination, from¹H nuclear magnetic resonance spectra, of those protons in a structure which are near in space to a selected, irradiated proton. The experiment is extremely powerful in the determination of structure in solution, and is sufficiently precise often to give stereochemical detail. The method was used in determination of the structures of the antibiotics of the teicoplanin complex (members of the vancomycin group), and the principles are briefly illustrated. Additionally, nuclear magnetic resonance pulse sequences can be used to edit¹³C spectra (separate the spectrum into four spectra, containing C, CH, CH₂, and CH₃ carbons), and this technique also aided the structure elucidation of the teicoplanin complex. Finally, it is emphasised that nuclear Overhauser effect difference spectroscopy can be used to determine the molecular details of drug binding sites, and an example is given.     

13C nmr study of the helix–coil transition of poly-N5-(3-hydroxypropyl)-L-glutamine

The helix–coil transition of poly-N⁵-(3-hydroxypropyl)-L -glutamine in methanol–water solutions has been observed using ¹³C nuclear magnetic resonance. Two signals appear in the α-CH region in the course of the transition; this is in contrast with previous proton magnetic resonance experiments carried out on this polymer in the same solvent system.     

Deletion of the carboxyl‐terminal residue disrupts the amino‐terminal folding,self‐association,and thermal stability of an amphipathic antimicrobial peptide

Understanding the complex relationship between amino acid sequence and protein behaviors, such as folding and self‐association, is a major goal of protein research. In the present work, we examined the effects of deleting a C‐terminal residue on the intrinsic properties of an amphapathic α‐helix of mastoparan‐B (MP‐B), an antimicrobial peptide with the sequence LKLKSIVSWAKKVL‐NH2. We used circular dichroism and nuclear magnetic resonance to demonstrate that the peptide MP‐B^[1‐13] displayed significant unwinding at the N‐terminal helix compared with the parent peptide of MP‐B, as the temperature increased when the residue at position 14 was deleted. Pulsed‐field gradient nuclear magnetic resonance data revealed that MP‐B forms a larger diffusion unit than MP‐B^[1‐13] at all experimental temperatures and continuously dissociates as the temperature increases. In contrast, the size of the diffusion unit of MP‐B^[1‐13] is almost independent of temperature. These findings suggest that deleting the flexible, hydrophobic amino acid from the C‐terminus of MP‐B is sufficient to change the intrinsic helical thermal stability and self‐association. This effect is most likely because of the modulation of enthalpic interactions and conformational freedom that are specified by this residue. Our results implicate terminal residues in the biological function of an antimicrobial peptide. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

A P Nuclear Magnetic Resonance Study of Intracellular pH of Plant Cells Cultivated in Liquid Medium

³¹P nuclear magnetic resonance has been used to study the vacuolar and cytoplasmic pH of Acer pseudoplatanus, Catharanthus roseus, and Glycine max cells grown as cell suspensions. The adaptation of this technique to plant cells grown in liquid medium is described with emphasis on the removal of Mn²⁺ and phosphate from the extracellular medium and on providing the O₂ supply of the cells in the nuclear magnetic resonance tube and the various problems of calibration. Aerobic and anaerobic cells show large differences in their glucose-6-phosphate, their cytoplasmic inorganic phosphate pools, and their cytoplasmic pH. Differences in the relative sizes of the cytoplasmic and vacuolar inorganic phosphate pools have been observed for the three cell strains studied.